Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01023789.1 Corchorus olitorius cultivar O-4 contig23822, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 11341
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33


Found at i:3278 original size:19 final size:18

Alignment explanation


    Indices: 3254--3289  Score: 54
    Period size: 19  Copynumber: 1.9  Consensus size: 18

       3244 TGAAGACTTA

                               
       3254 TTGAAGACAATTTGAAGAT
          1 TTGAAGACAA-TTGAAGAT

                    *        
       3273 TTGAAGACCATTGAAGA
          1 TTGAAGACAATTGAAGA

       3290 ATTATTTCCA


Statistics
Matches: 16,  Mismatches: 1, Indels: 1
        0.89            0.06        0.06

Matches are distributed among these distances:
  18    7  0.44
  19    9  0.56

ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28


Consensus pattern (18 bp):   
TTGAAGACAATTGAAGAT

Found at i:5078 original size:28 final size:27

Alignment explanation


    Indices: 5046--5098  Score: 72
    Period size: 28  Copynumber: 1.9  Consensus size: 27

       5036 ACAAAGATTA

                                         
       5046 AAAACGCAAAATCAAAT-TTTTTTTAGTG
          1 AAAACGCAAAA--AAATATTTTTTTAGTG

                    *                
       5074 AAAACGCAGAAAAATATTTTTTTAG
          1 AAAACGCAAAAAAATATTTTTTTAG

       5099 ATCATAAACG


Statistics
Matches: 23,  Mismatches: 1, Indels: 3
        0.85            0.04        0.11

Matches are distributed among these distances:
  26    4  0.17
  27    9  0.39
  28   10  0.43

ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34


Consensus pattern (27 bp):   
AAAACGCAAAAAAATATTTTTTTAGTG

Found at i:5107 original size:29 final size:26

Alignment explanation


    Indices: 5059--5112  Score: 72
    Period size: 27  Copynumber: 2.0  Consensus size: 26

       5049 ACGCAAAATC

                          *           
       5059 AAATTTTTTTTAGTGAAAACGCAGAA
          1 AAATTTTTTTTAGTCAAAACGCAGAA

                                        
       5085 AAATATTTTTTTAGATCATAAACGCAGA
          1 AAAT-TTTTTTTAG-TCA-AAACGCAGA

       5113 GACTGAGAAA


Statistics
Matches: 24,  Mismatches: 1, Indels: 3
        0.86            0.04        0.11

Matches are distributed among these distances:
  26    4  0.17
  27    9  0.38
  28    2  0.08
  29    9  0.38

ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35


Consensus pattern (26 bp):   
AAATTTTTTTTAGTCAAAACGCAGAA
Done.